A novel coarse-grained energy functions for RNA folding

Coarse-grained models combined with effective sampling techniques are now poised to address a wide range of problems in biological systems. An accurate coarse-grained force field is crucial for quantitative modeling of structure, dynamics, and function. We recently developed a novel approach to extract RNA coarse-grained energy functions from the structural database. The key ingredient of the approach is to stepwise build the correlations between the different interactions and the inherent chain connectivity and excluded volume interactions through an iterative construction of the reference states. The novel approach allows us to extract energy functions from the inverse Boltzmann law. The validity of this approach is supported by the close agreement between the simulated distributions for all the structural parameters and those observed from the experimental structure database. Benchmark tests on tertiary structure folding and 3D structure predictions show comparable or much improved predictions than existing coarse-grained models. This novel method for the treatment of many-body correlation effects can be easily transferred to other computational biology problems.